Mercurial > repos > mingchen0919 > tripal_db_explorer

<tool id="es_gene_search" name="tripal_db_explorer: elasticsearch gene search" version="1.0.0">
  <description>  </description>
  <requirements>
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement><requirement type="package" version="1.20.0">r-getopt</requirement><requirement type="package" version="1.6">r-rmarkdown</requirement><requirement type="package" version="1.5">r-jsonlite</requirement><requirement type="package" version="0.2">r-dt</requirement><requirement type="package" version="3.1">r-curl</requirement><requirement type="package" version="1.95_4.8">r-rcurl</requirement></requirements>
  <stdio>
        <regex match="XXX" source="stderr" level="warning" description="Check the warnings_and_errors.txt file for more details."/></stdio>
  <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&

Rscript '${__tool_directory__}/'es_gene_search_render.R

	-o '$report'
	-d '$report.files_path'
	-U '$tripal_db_url'
	-O '$organism'
	-K '$search_keywords'
	-R '$fasta_results'
]]></command>
  <inputs>
        <param type="text" name="tripal_db_url" label="Tripal database URL" optional="False"/><param type="text" name="organism" label="Organism" optional="False"/><param type="text" name="search_keywords" label="Search keywords" optional="False"/><param type="boolean" name="download_fasta" label="Save gene sequences to fasta file" optional="False" truevalue="TRUE" falsevalue="FALSE"/></inputs>
  <outputs>
        <data name="report" format="html" label="${tool.name} report" hidden="false"/><data name="sink_message" format="txt" label="${tool.name} log" from_work_dir="warnings_and_errors.txt" hidden="false"/><data name="fasta_results" format="fasta" label="${tool.name} results" hidden="false"/></outputs>
  <citations>
        <citation type="bibtex"><![CDATA[
            @article{allaire2016rmarkdown,
            title={rmarkdown: Dynamic Documents for R, 2016},
            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
            journal={R package version 0.9},
            volume={6},
            year={2016}
            }
        ]]></citation><citation type="bibtex"><![CDATA[
            @book{xie2015dynamic,
            title={Dynamic Documents with R and knitr},
            author={Xie, Yihui},
            volume={29},
            year={2015},
            publisher={CRC Press}
            }
        ]]></citation></citations>
</tool>
author	mingchen0919
date	Mon, 19 Mar 2018 22:44:25 -0400
parents	dbe86b15ee8b
children